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  • Jan 31 22:52
    matq007 commented #261
  • Jan 31 22:49
    matq007 edited #261
  • Jan 31 22:46
    matq007 opened #261
  • Jan 31 14:33
    ewels edited #252
  • Jan 31 14:33
    ewels commented #252
  • Jan 31 13:29
    pachiras commented #252
  • Jan 31 12:34
    matq007 assigned #252
  • Jan 31 11:53
    apeltzer commented #252
  • Jan 31 10:51
    matq007 commented #252
  • Jan 31 08:22
    apeltzer commented #252
  • Jan 31 02:13
    pachiras commented #252
  • Jan 29 20:42
    af8 starred nf-core/tools
  • Jan 29 08:47

    nf-core-bot on api-doc

    Travis build: 816 (compare)

  • Jan 29 08:42

    apeltzer on dev

    Markdown parsing: Fix all the e… Add new markdown rules to templ… Apparently whitespace isn't eno… and 2 more (compare)

  • Jan 29 08:42
    apeltzer closed #260
  • Jan 28 23:42
    ewels synchronize #260
  • Jan 28 23:07
    ewels synchronize #260
  • Jan 28 22:57
    ewels synchronize #260
  • Jan 28 22:57
    ewels review_requested #260
  • Jan 28 22:57
    ewels review_requested #260
Alexander Peltzer
@apeltzer
Also we’ve moved to slack in nf core :-)
Paolo Di Tommaso
@pditommaso
I guess he confused it for NF channel
Alexander Peltzer
@apeltzer
Yes :-)
Phil Ewels
@ewels
I wonder if we should close this chat group to avoid future confusion... :/
For future readers: Reminder that we have moved to Slack. See nf-co.re to get an invite (top right of any page) or visit https://nf-core-invite.herokuapp.com/ directly.
Alexander Peltzer
@apeltzer
Yes - makes sense, alreay put up the info in the header too
sureshhewa
@sureshhewabi
Can nextflow log file location customized by passing as a params?
Alexander Peltzer
@apeltzer
Reminder that we have moved to Slack. See nf-co.re to get an invite (top right of any page) or visit https://nf-core-invite.herokuapp.com/ directly.
:smile:
Phil Ewels
@ewels
Also this is for nf-core, not to be confused with the gitter channel for nextflow itself: https://gitter.im/nextflow-io/nextflow
Michael L Heuer
@heuermh
@apeltzer Considering moving back to Gitter? I didn't come with because Slack disagrees with me.
Phil Ewels
@ewels
Not going to happen sorry @heuermh. There's too much discussion for gitter, it was impossible to keep track of the different threads. With slack we can have everyone in one place but split in to the different channels, also with threads in each channel. The difference has been huge.
We did have a look around at other solutions too, eg. Zulip and others. We didn't like them as much as Slack though..
What's wrong with Slack for you? I guess while we keep this gitter channel open we can always use both.. There's a mailing list too.
Michael L Heuer
@heuermh
@ewels I'm spread across too many projects for Slack to be workable on a daily basis. With Gitter there is good Github integration and it's not too unreasonable to follow many different projects. I'll try to catch up with nf-core at BOSC and/or the CoFest!
Phil Ewels
@ewels
Ok, understandable. There's always tools like https://slackdigest.com/ ;) But yes - there should be a few people at BOSC / CoFest / ISMB..
RationalTangle
@RationalTangle
I really appreciate the work you've all done already but is anyone interested in starting a conversation about how to add contaminant filtering/identification/visualization to the preprocessing pipeline of nf-core/rna-seq? It's a problem I'm currently dealing with and it feels like something that should be included in nf-core.
I know there are already old feature requests for adding salmon/kallisto and differential expression analysis, so I realize it might spread dev focus too thin
I'm new to nextflow, nf-core, and processing rna-seq data in general. Nevertheless, if my attempts to automate my own process could be folded into nf-core I'd be happy to help
Alexander Peltzer
@apeltzer
You found the Slack already @RationalTangle ;-) Either there or open an issue on GitHub in the nf-core/rnaseq repository :-)
Given how much questions / discussion points yuo have, maybe an issue to have the discussion streamlind would be a good start :+1:
Leon-Bichmann
@Leon-Bichmann
yld: Library not loaded: /usr/local/opt/readline/lib/libreadline.7.dylib
Referenced from: /usr/local/bin/awk
Reason: image not found
ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 8 or later is installed
NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:
JAVA_CMD: /Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Home/bin/java
JAVA_HOME: /Library/Java/JavaVirtualMachines/jdk-12.0.1.jdk/Contents/Home
both JAVA_CMD and HOME directories are correct
Leon-Bichmann
@Leon-Bichmann
problem solved there was a problem with the gawk installation
Combiz
@combiz_k_twitter
Hi if anybody could take a look at the question I posted on the google groups page that would be much appreciate: https://groups.google.com/forum/#!topic/nextflow/TnTxv4iMm88
Alexander Peltzer
@apeltzer
That might be a question for the nextflow channel
We also migrated to slack for Nf-core entirely
Combiz
@combiz_k_twitter
Thanks Alexander
Phil Ewels
@ewels
Yes, this is nf-core - the nextflow gitter channel is here: https://gitter.im/nextflow-io/nextflow
Combiz
@combiz_k_twitter
Is there a list anywhere defining 'nf-core best practices'? There's a lot going on in the template folder generated by nf-core create, a text description would be useful..
Phil Ewels
@ewels
Hello! Slack is better, nf-core Gitter is depreciated really (I should delete it..?)
But no, no description of the files in the template yet.
That’s a great idea!
If you could make an issue on the website repo, then we can definitely take a look into it
Or maybe as part of the documentation for the tools package..?
Combiz
@combiz_k_twitter
@ewels Thanks for the reply Phil, sure I'll add the issue on the repo